def create_github_repo(dataset, repo_name):
"""Setup a github sibling / remote."""
try:
# raise exception if github exports are not enabled
if not DATALAD_GITHUB_EXPORTS_ENABLED:
raise Exception(
'DATALAD_GITHUB_EXPORTS_ENABLED must be defined to create remote repos')
# this adds github remote to config and also creates repo
return create_sibling_github(repo_name,
github_login=DATALAD_GITHUB_LOGIN,
github_passwd=DATALAD_GITHUB_PASS,
github_organization=DATALAD_GITHUB_ORG,
dataset=dataset,
access_protocol='ssh')
except KeyError:
raise Exception(
'DATALAD_GITHUB_LOGIN, DATALAD_GITHUB_PASS, and DATALAD_GITHUB_ORG must be defined to create remote repos')
def add(
template_id,
osf_user,
osf_password,
osf_overwrite,
gh_user,
gh_token,
path,
nprocs,
):
"""Add a new template."""
from .io import run_command
from .utils import copy_template
import shutil
from datalad import api as dl
gh_password = getenv("GITHUB_PASSWORD")
if not gh_user or not gh_token:
raise click.BadParameter("Insufficient secrets to login into GitHub")
path = Path(path or f"tpl-{template_id}").absolute()
cwd = Path.cwd()
if not path.exists():
raise click.UsageError(f"<{path}> does not exist.")
metadata = {}
# Check metadata
if (path / "template_description.json").exists():
metadata = json.loads((path / "template_description.json").read_text())
metadata["Identifier"] = template_id
# Check license
license_path = path / "LICENSE"
if not license_path.exists():
license_path = path / "LICENCE"
if not license_path.exists():
license_path = path / "COPYING"
if not license_path.exists():
license_prompt = click.prompt(
text="""\
A LICENSE file MUST be distributed with the template. The TemplateFlow Manager can \
set a license (either CC0 or CC-BY) for you.""",
type=click.Choice(("CC0", "CC-BY", "Custom (abort)")),
default="Custom (abort)",
)
if license_prompt == "Custom (abort)":
raise click.UsageError(
"Cannot proceed without a valid license. Please write a LICENSE "
"file before uploading.")
license_path = Path(
pkgr_fn("tfmanager", f"data/{license_prompt}.LICENSE"))
metadata["License"] = license_prompt
# Check RRID
if not metadata.get("RRID"):
rrid = click.prompt(
text="Has a RRID (research resource ID) already been assigned?",
type=str,
default='') or None
if rrid:
metadata["RRID"] = rrid
# Check short description
if not metadata.get("Name", "").strip():
short_desc = click.prompt(
text="""\
The "Name" metadata is not found within the <template_description.json> file. \
Please provide a short description for this resource.""",
type=str,
)
if not short_desc:
raise click.UsageError(
"Cannot proceed without a short description.")
metadata["Name"] = short_desc
# Check authors
authors_prompt = [
a.strip() for a in metadata.get("Authors", []) if a.strip()
]
if not authors_prompt:
authors_prompt = [
n.strip() for n in click.prompt(
text="""\
The "Authors" metadata is not found within the <template_description.json> file. \
Please provide a list of authors separated by semicolon (;) in <Lastname Initial(s)> format.""",
type=str,
).split(";") if n
]
if not authors_prompt:
click.confirm("No authors were given, do you want to continue?",
abort=True)
metadata["Authors"] = authors_prompt
# Check references
refs_prompt = [
f"""\
{'https://doi.org/' if not a.strip().startswith('http') else ''}\
{a.replace("doi:", "").strip()}"""
for a in metadata.get("ReferencesAndLinks", []) if a.strip()
]
if not refs_prompt:
refs_prompt = [
n.replace('"', "").strip() for n in click.prompt(
text="""\
The "ReferencesAndLinks" metadata is not found within the <template_description.json> file. \
Please provide a list of links and publications within double-quotes \
(for example, "doi:10.1101/2021.02.10.430678") and separated by spaces (< >).""",
type=str,
).split(" ") if n
]
if not refs_prompt:
click.confirm("No authors were given, do you want to continue?",
abort=True)
metadata["ReferencesAndLinks"] = refs_prompt
with TemporaryDirectory() as tmpdir:
repodir = Path(tmpdir) / "templateflow"
# Clone root <user>/templateflow project - fork if necessary
click.echo(f"Preparing Pull-Request (wd={tmpdir}).")
clone = run_command(
f"git clone https://github.com/{gh_user}/templateflow.git "
"--branch tpl-intake --single-branch",
cwd=tmpdir,
capture_output=False,
)
if clone.returncode != 0:
run_command(
"hub clone templateflow/templateflow",
cwd=tmpdir,
capture_output=False,
env={
"GITHUB_USER": gh_user,
"GITHUB_PASSWORD": gh_password
},
)
run_command(
"hub fork --remote-name origin",
cwd=str(repodir),
capture_output=False,
env={
"GITHUB_USER": gh_user,
"GITHUB_PASSWORD": gh_password
},
)
else:
run_command(
"git remote add upstream https://github.com/templateflow/templateflow.git",
cwd=str(repodir),
capture_output=False,
)
chdir(repodir)
# Create datalad dataset
dl.create(
path=f"tpl-{template_id}",
cfg_proc="text2git",
initopts={"initial-branch": "main"},
description=metadata["Name"],
)
# Populate template
copy_template(
path=path,
dest=repodir / f"tpl-{template_id}",
)
# Copy license
shutil.copy(license_path, repodir / f"tpl-{template_id}" / "LICENSE")
# (Over)write template_description.json
(repodir / f"tpl-{template_id}" /
"template_description.json").write_text(json.dumps(metadata,
indent=2))
# Init/update CHANGELOG
changelog = repodir / f"tpl-{template_id}" / "CHANGES"
changes = [
f"""
## {datetime.date.today().ctime()} - TemplateFlow Manager Upload
Populated contents after NIfTI sanitizing by the TF Manager.
"""
]
if changelog.exists():
changes += [changelog.read_text()]
changelog.write_text("\n".join(changes))
# Init OSF sibling
rrid_str = f" (RRID: {metadata['RRID']})" if metadata.get(
"RRID") else ""
dl.create_sibling_osf(
title=f"TemplateFlow resource: <{template_id}>{rrid_str}",
name="osf",
dataset=f"./tpl-{template_id}",
public=True,
category="data",
description=metadata["Name"],
tags=["TemplateFlow dataset", template_id])
# Init GH sibling
dl.create_sibling_github(reponame=f"tpl-{template_id}",
dataset=str(repodir / f"tpl-{template_id}"),
github_login=gh_user,
publish_depends="osf-storage",
existing="replace",
access_protocol="ssh")
# Save added contents
dl.save(dataset=str(repodir / f"tpl-{template_id}"),
message="ADD: TemplateFlow Manager initialized contents")
# Push to siblings
dl.push(
dataset=str(repodir / f"tpl-{template_id}"),
to="github",
jobs=cpu_count(),
)
# Back home
chdir(cwd)
run_command(
"git fetch upstream tpl-intake",
cwd=str(repodir),
capture_output=False,
)
run_command(
f"git checkout -b pr/tpl-{template_id} upstream/tpl-intake",
cwd=str(repodir),
capture_output=False,
)
(repodir / f"{path.name}.toml").write_text(
toml.dumps({
"github": {
"user": gh_user
},
}))
run_command(
f"git add {path.name}.toml",
cwd=str(repodir),
capture_output=False,
)
run_command(
f"git commit -m 'add(tpl-{template_id}): create intake file'",
cwd=str(repodir),
capture_output=False,
)
run_command(
f"git push -u origin pr/tpl-{template_id}",
cwd=str(repodir),
capture_output=False,
env={
"GITHUB_USER": gh_user,
"GITHUB_TOKEN": gh_token
},
)
(repodir.parent / "message.md").write_text(f"""\
ADD: ``tpl-{template_id}``
## {metadata.get('Name', '<missing Name>')}
Identifier: {metadata.get('Identifier', '<missing Identifier>')}
Datalad: https://github.com/{gh_user}/tpl-{template_id}
### Authors
{', '.join(metadata['Authors'])}.
### License
{metadata.get('License', metadata.get('Licence', '<missing License>'))}
### Cohorts
{' '.join(('The dataset contains', str(len(metadata.get('cohort', []))), 'cohorts.'))
if metadata.get('cohort') else 'The dataset does not contain cohorts.'}
### References and links
{', '.join(metadata.get('ReferencesAndLinks', [])) or 'N/A'}
""")
run_command(
"hub pull-request -b templateflow:tpl-intake "
f"-h {gh_user}:pr/tpl-{template_id} "
f"-F {repodir.parent / 'message.md'}",
cwd=str(repodir),
capture_output=False,
env={
"GITHUB_USER": gh_user,
"GITHUB_TOKEN": gh_token
},
)